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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCCAAGATGGTGACGCCTCTCATCAAGCGCGATGTCGTCAAGAAGCGGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaactcttcatgaacattttccgtttttttttttctttttcttttttttttttttttttttttttttttttttttgccgtttctcctccgtgct...

Basic information

species Physcomitrella patens
transcript PP1S98_19V6.1
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18333387|gb|BJ165401.1|BJ165401
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162232234|gb|FC408070.1|FC408070
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18329113|gb|BJ161119.1|BJ161119
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18359014|gb|BJ191074.1|BJ191074
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18349181|gb|BJ181230.1|BJ181230
EST:     TCAAGANGTTCAGAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: TCAAGAAGTTCA-AGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18332553|gb|BJ164566.1|BJ164566
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|208381398|gb|DC927834.1|DC927834
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|67697693|gb|BJ957926.1|BJ957926
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18336143|gb|BJ168165.1|BJ168165
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162233982|gb|FC410300.1|FC410300
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|7648418|gb|AW739401.1|AW739401
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162205354|gb|FC382063.1|FC382063
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18349959|gb|BJ182010.1|BJ182010
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162279864|gb|FC455148.1|FC455148
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|67696979|gb|BJ957212.1|BJ957212
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|67726861|gb|BJ977120.1|BJ977120
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|208353930|gb|DC914084.1|DC914084
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162276296|gb|FC452104.1|FC452104
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162230913|gb|FC406752.1|FC406752
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18332458|gb|BJ164471.1|BJ164471
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|6102150|gb|AW126620.1|AW126620
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|67574284|gb|BJ947108.1|BJ947108
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|37852413|gb|BJ610421.1|BJ610421
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162279251|gb|FC455798.1|FC455798
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18341795|gb|BJ173830.1|BJ173830
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|37828930|gb|BJ586942.1|BJ586942
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|67718387|gb|BJ968646.1|BJ968646
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162227277|gb|FC402868.1|FC402868
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162212773|gb|FC388573.1|FC388573
EST:     GCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162232233|gb|FC408069.1|FC408069
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18327908|gb|BJ159912.1|BJ159912
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18325433|gb|BJ157429.1|BJ157429
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|37820943|gb|BJ579009.1|BJ579009
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162205049|gb|FC381758.1|FC381758
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACAAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|18341873|gb|BJ173908.1|BJ173908
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|162279250|gb|FC455797.1|FC455797
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
EST: gi|67573594|gb|BJ946418.1|BJ946418
EST:     GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAG                         ACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC
genomic: GGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 31

ATCTGCCAAGATGGTGACGCCTCTCATCAAGCGCGATGTCGTCAAGAAGCGGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaac ... tctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTCAAAGGCACTACTTTGATGCCCAACATTGGTTACGGCTCAAACAAGAAGA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCCAAGATGGTGACGCCTCTCATCAAGCGCGATGTCGTCAAGAAGCGGGTCAAGAAGTTCAAGCGCATGCAGTCTGACCGCAAGATTTGCGTGAAGgtattgaaactcttcatgaacattttccgtttttttttttctttttcttttttttttttttttttttttttttttttttttgccgtttctcctccgtgct

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA